# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-scores hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1dnlA 199 4.38e-35 1ci0A b.45.1.1 25753 1g79A 218 4.74e-35 1ci0A b.45.1.1 25752 1nrgA 261 4.43e-30 b.45.1.1 80694 1t9mA 214 7.23e-26 1ty9A 222 1.84e-24 1ci0A 228 1.71e-23 1ci0A b.45.1.1 25750 1rfeA 162 2.22e-14 2fhqA 141 3.82e-14 1vl7A 157 9.22e-11 b.45.1.1 108732 2fg9A 178 5.84e-10 2aq6A 147 6.83e-09 2asfA 137 1.14e-08 1w9aA 147 2.86e-08 1xxoA 147 4.00e-08 2arzA 247 2.73e-06 2furA 209 6.32e-06 1xhnA 184 6.99e-06 1axj 122 9.51e-05 1axj b.45.1.1 25749 1flmA 122 1.28e-04 1axj b.45.1.1 25747 1w3oA 216 1.52e-03 1ejeA 192 3.18e-02 1ejeA b.45.1.2 25757 1m1hA 248 4.79e-02 b.114.1.1,d.58.42.1 78415,78416 1ujmA 342 5.40e-01 1y1pA 342 5.69e-01 1nar 290 6.22e-01 1nar c.1.8.5 28988 2bgiA 272 9.59e-01 2bh8A 101 1.05e+00 1p9bA 442 1.10e+00 c.37.1.10 94385 1widA 130 1.34e+00 1wj9A 211 1.51e+00 1ryp2 233 1.98e+00 1ryp2 2a6sA 84 2.08e+00 1j5yA 187 2.32e+00 a.4.5.1,d.94.2.1 71592,71593 1qp2A 70 2.80e+00 1pse b.34.4.2 24596 1v6fA 151 2.91e+00 d.109.1.2 108395 1k68A 140 3.06e+00 c.23.1.1 90943 2bgzA 299 3.12e+00 1wlgA 299 3.24e+00 1bc8C 93 3.30e+00 1awcA a.4.5.21 16168 1jdqA 98 3.80e+00 d.68.3.3 66559 1a1aA 107 3.86e+00 1fmk d.93.1.1 40449 1zt3A 80 4.22e+00 1vkkA 154 4.26e+00 d.109.1.2 108669 1a7j 290 4.29e+00 1a7j c.37.1.6 31952 2ag5A 246 4.36e+00 1btl 263 4.57e+00 1btl e.3.1.1 42691 1fqgA 263 4.61e+00 1btl e.3.1.1 42699 1m40A 263 4.62e+00 e.3.1.1 74437 1ermA 263 4.87e+00 1btl e.3.1.1 42690 1mwsA 646 4.92e+00 d.17.4.5,d.175.1.1,e.3.1.1 79592,79593,79594 1pysA 350 5.01e+00 1pysA d.104.1.1 40775 1ibvB 229 5.01e+00 1cauB 184 5.05e+00 1caxB b.82.1.2 28103 1g0uE 234 5.14e+00 d.153.1.4 41950 1pyaB 228 5.59e+00 1pyaB 1txyA 104 5.78e+00 1mjc 69 6.08e+00 1mjc b.40.4.5 25319 2fp8A 322 6.35e+00 1b7yA 350 6.51e+00 1pysA d.104.1.1 40776 1bax 94 6.59e+00 1bax a.61.1.3 18133 2f6kA 307 7.12e+00 1pauA 147 7.19e+00 1pauA c.17.1.1 30994 1g0u1 266 7.33e+00 1dgrV 79 7.47e+00 1caxB b.82.1.2 28099 1wcdJ 441 7.76e+00 1eziA 228 7.85e+00 1eyrA c.68.1.13 34512 2ebn 289 7.88e+00 2ebn c.1.8.5 28990 1dgrN 79 8.25e+00 1caxB 1ygtA 111 8.64e+00 1nmeA 146 8.68e+00 c.17.1.1 85874 1qba 858 8.89e+00 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21810,22406,29009,40408 1rypF 233 8.91e+00 1rypF d.153.1.4 41937 1ywxA 102 9.00e+00 1am2 199 9.39e+00 1am2 b.86.1.2 28381 1ae3 86 9.55e+00 1gvp b.40.4.7 25381 1prr 173 9.57e+00 1prs b.11.1.1,b.11.1.1 23623,23624 1q5qA 259 1.02e+01 d.153.1.4 95904 1shdA 107 1.03e+01 1fmk d.93.1.1 40440 1ivd 388 1.05e+01 2qwc b.68.1.1 27568 2bitX 165 1.06e+01 1mkmA 249 1.07e+01 a.4.5.33,d.110.2.2 79242,79243 1vm8A 534 1.07e+01 2bduA 297 1.11e+01 2a1fA 247 1.12e+01 3mefA 69 1.15e+01 1mjc b.40.4.5 25320 1f0iA 504 1.21e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 2g09A 297 1.22e+01 1v0wA 506 1.22e+01 d.136.1.2,d.136.1.2 108220,108221 1d02A 202 1.23e+01 1d02A c.52.1.8 33313 1b8aA 438 1.26e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1o4rA 108 1.27e+01 d.93.1.1 92469 1ye8A 178 1.30e+01 1gvp 87 1.32e+01 1gvp b.40.4.7 25369 1nrkA 328 1.32e+01 b.44.2.1,d.250.1.1 92089,92090 1vqb 87 1.34e+01 1gvp b.40.4.7 25370 2gnoA 305 1.35e+01 1rgzA 363 1.40e+01 e.3.1.1 97457 1tvjA 166 1.41e+01 1td5A 202 1.42e+01 d.110.2.2 106767 1r1bA 59 1.43e+01 1r1bA a.16.1.3 16396 1pbyA 489 1.44e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1i35A 95 1.46e+01 d.15.1.5 66017 1ei1A 391 1.49e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1tplA 426 1.51e+01 1ax4A c.67.1.2 34387 1ylnA 252 1.51e+01 1vlyA 338 1.52e+01 b.44.2.1,d.250.1.1 108871,108872 1si6X 282 1.53e+01 1w3fA 315 1.53e+01 1ntfA 282 1.54e+01 d.151.1.2 92104 1y21A 282 1.54e+01 1c7sA 858 1.62e+01 1qba b.1.18.2,b.2.2.3,c.1.8.6,d.92.2.1 21812,22408,29011,40410 1pse 69 1.63e+01 1pse b.34.4.2 24595 1prs 173 1.67e+01 1prs b.11.1.1,b.11.1.1 23625,23626 2c60A 111 1.67e+01 1b7gO 340 1.67e+01 1b7gO c.2.1.3,d.81.1.1 29992,39907 1shbA 104 1.72e+01 1fmk d.93.1.1 40425 1wi1A 126 1.74e+01 1eyrA 228 1.75e+01 1eyrA c.68.1.13 34514 1zkpA 268 1.77e+01 1ga0A 364 1.81e+01 1gceA e.3.1.1 60410 1di2A 69 1.85e+01 1di2A d.50.1.1 38780 1f2fA 104 1.89e+01 1fmk d.93.1.1 40455 1fofA 246 1.90e+01 1fofA e.3.1.1 42763 1r2zA 274 1.93e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1uf2C 421 1.93e+01 a.115.1.3,b.19.1.1 99291,99292 1cl1A 395 1.94e+01 1cl2A c.67.1.3 34395 1shaA 104 1.96e+01 1fmk d.93.1.1 40424 1l1zA 274 1.98e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 1nqkA 381 2.01e+01 c.1.16.4 92050 1h6fA 193 2.02e+01 b.2.5.4 70901 2fe7A 166 2.03e+01 1qmyA 167 2.10e+01 1qmyA d.3.1.2 37094 1wrmA 165 2.10e+01 1onhA 364 2.11e+01 e.3.1.1 93357 1d8hA 311 2.18e+01 1d8iA d.63.1.1 39544 1cp3A 277 2.20e+01 1pauA c.17.1.1 30992 1caxB 184 2.21e+01 1caxB b.82.1.2 28105 1gceA 364 2.22e+01 1gceA e.3.1.1 42738 2hts 88 2.25e+01 2hts a.4.5.22 16174 1rocA 155 2.32e+01 b.1.22.1 97673 2ddrA 306 2.32e+01 1xv2A 237 2.35e+01 1d2dA 59 2.35e+01 1r1bA a.16.1.3 16397 1aazA 87 2.40e+01 1aba c.47.1.1 32761 2bltA 361 2.41e+01 1gceA e.3.1.1 42739 1h7zA 194 2.43e+01 1qhvA b.21.1.1 60733 1vhtA 218 2.45e+01 c.37.1.1 100700 1ezwA 349 2.48e+01 1ezwA c.1.16.3 29558 1ollA 188 2.48e+01 b.1.1.4,b.1.1.4 93313,93314 1d2fA 390 2.50e+01 1d2fA c.67.1.3 34411 2bc4A 211 2.52e+01 2avtA 378 2.56e+01 1wocA 103 2.57e+01 1pgvA 197 2.61e+01 c.10.1.1 88073 1tf5A 844 2.61e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1r0wA 286 2.62e+01 c.37.1.12 96754 1j5kA 89 2.62e+01 d.51.1.1 71565 1gutA 68 2.63e+01 b.40.6.1 65576 2cavA 445 2.81e+01 1dgwA b.82.1.2,b.82.1.2 28094,28095 1k55A 246 2.83e+01 e.3.1.1 68156 1aba 87 2.83e+01 1aba c.47.1.1 32760 1gnwA 211 2.83e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1bypA 99 2.84e+01 1plc b.6.1.1 22858 1j71A 334 2.86e+01 1eagA b.50.1.2 62669 1e3uA 246 2.87e+01 1fofA e.3.1.1 42755 1sacA 204 2.91e+01 1sacA b.29.1.5 24237 1fmk 452 2.92e+01 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1iweA 457 2.93e+01 c.37.1.10 71486 1y89A 238 2.94e+01 1cs1C 386 2.95e+01 1ibjA c.67.1.3 34401 1lrv 244 2.99e+01 1lrv a.118.1.5 19146 1mxiA 160 2.99e+01 c.116.1.1 79646 2gcfA 73 3.00e+01 1t0bA 252 3.01e+01 c.23.16.6 106199 2f15A 96 3.02e+01 1p5tA 127 3.04e+01 b.55.1.2 94148 1vqqA 646 3.06e+01 2rspB 124 3.10e+01 2rspB b.50.1.1 26772 1vdnA 162 3.11e+01 1wsrA 375 3.13e+01 1scjB 71 3.20e+01 1scjB d.58.3.2 39069 1v1qA 134 3.28e+01 1hdmA 201 3.28e+01 1iakA b.1.1.2,d.19.1.1 21583,38157 2bwrA 401 3.29e+01 1nhyA 219 3.29e+01 a.45.1.1,c.47.1.5 80520,80521 1cs1A 386 3.32e+01 1ibjA c.67.1.3 34399 2g40A 224 3.35e+01 1gfsA 321 3.38e+01 c.2.1.2 29811 1mvpA 124 3.42e+01 2rspB b.50.1.1 26775 1msaA 109 3.58e+01 1b2pA b.78.1.1 27987 2f9dA 125 3.60e+01 2rspA 124 3.69e+01 2rspB b.50.1.1 26771 1ivg 388 3.70e+01 2qwc b.68.1.1 27578 2c07A 285 3.71e+01 1cl2A 395 3.76e+01 1cl2A c.67.1.3 34397 1k66A 149 3.78e+01 c.23.1.1 90941 1f6kA 293 3.81e+01 1nal3 c.1.10.1 29081 1dixA 208 3.82e+01 1bk7A d.124.1.1 41122 2axoA 270 3.87e+01 3htsB 102 3.97e+01 2hts a.4.5.22 16175 1f3uA 118 4.01e+01 1f3uA b.65.1.1 27521 1rz3A 201 4.02e+01 c.37.1.6 98132 1i3cA 149 4.03e+01 c.23.1.1 71112 1wbsA 360 4.05e+01 1s5jA 847 4.11e+01 1jjuA 489 4.17e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1c7gA 456 4.18e+01 c.67.1.2 90415 1f74A 293 4.18e+01 1nal3 c.1.10.1 29079 1ualA 274 4.20e+01 c.116.1.4 88383 1oz9A 150 4.26e+01 d.92.1.15 93808 1oflA 481 4.29e+01 b.80.1.4 103934 1rl6A 177 4.31e+01 1rl6A d.141.1.1,d.141.1.1 41473,41474 1gvjA 146 4.34e+01 a.4.5.21 90525 1a0rB 340 4.37e+01 1tbgA b.69.4.1 27658 1ha1 184 4.40e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 3hsf 92 4.52e+01 2hts a.4.5.22 16182 1ay2 159 4.53e+01 2pil d.24.1.1 38377 1k4fA 248 4.57e+01 e.3.1.1 68138 2pil 159 4.74e+01 2pil d.24.1.1 38376 1aquA 297 4.74e+01 1aquA c.37.1.5 31942 1rypE 242 4.77e+01 1rypE d.153.1.4 41936 1n87A 56 4.87e+01 g.44.1.2 85390 1dgwX 79 4.98e+01 1caxB b.82.1.2 28091 2av1A 275 5.05e+01 1h4rA 314 5.07e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1qfjA 232 5.10e+01 1qfjA b.43.4.2,c.25.1.1 25655,31545 1x88A 359 5.10e+01 1aroP 883 5.15e+01 1cezA e.8.1.3 43112 1rzrA 332 5.21e+01 1drw 273 5.25e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1pbk 116 5.27e+01 1fkj d.26.1.1 38428 1an7A 136 5.28e+01 1seiA d.140.1.1 41465 1z4xA 532 5.29e+01 2a1kA 233 5.31e+01 1bwsA 321 5.33e+01 1bsvA c.2.1.2 29812 1bkf 107 5.34e+01 1fkj d.26.1.1 38382 1qrrA 394 5.40e+01 1qrrA c.2.1.2 29824 1dih 273 5.40e+01 1drw c.2.1.3,d.81.1.3 30056,39971 1jv1A 505 5.44e+01 c.68.1.5 71892 1t8sA 484 5.50e+01 c.56.2.1 106679 1wxcA 281 5.50e+01 1t77A 414 5.54e+01 1mxgA 435 5.57e+01 b.71.1.1,c.1.8.1 85193,85194 1ae2 87 5.58e+01 1gvp b.40.4.7 25382 1i24A 404 5.69e+01 c.2.1.2 83663 1qa7A 217 5.72e+01 1havA b.47.1.4 26425 2cn3A 737 5.74e+01 1zx5A 300 5.74e+01 1wi6A 88 5.74e+01 1ywrA 360 5.75e+01 1tr8A 102 5.76e+01 1qk8A 146 5.79e+01 1ewxA c.47.1.10 33061 1b04A 318 5.81e+01 1b04A d.142.2.2 41579 2bayA 61 5.92e+01 1lepA 99 5.94e+01 1lepA b.35.1.1 24649 1sxgA 280 5.98e+01 1ta8A 332 5.99e+01 1z4vA 532 6.13e+01 1o8xA 146 6.20e+01 c.47.1.10 86681 1a8p 258 6.21e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1d2mA 665 6.22e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1cvrA 435 6.23e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2d0oA 610 6.27e+01 2a74A 643 6.33e+01 1dzrA 183 6.37e+01 1dzrA b.82.1.1 28076 1ewxA 146 6.37e+01 1ewxA c.47.1.10 33062 1fvaA 217 6.44e+01 1fvaA d.58.28.1 39409 1jyoE 105 6.44e+01 d.184.1.2 67487 1kqnA 279 6.46e+01 c.26.1.3 77492 1j8uA 325 6.51e+01 d.178.1.1 71611 1ajyA 71 6.51e+01 1zmeC g.38.1.1,h.1.3.1 45083,45516 1mdyA 68 6.55e+01 1mdyA a.38.1.1 17132 1spbP 78 6.56e+01 1scjB d.58.3.2 39068 1ukgA 252 6.57e+01 b.29.1.1 99489 1w0pA 781 6.57e+01 b.29.1.8,b.29.1.8,b.68.1.1 109038,109039,109040 1n3oA 252 6.58e+01 b.29.1.1 79967 2av7A 275 6.61e+01 1t7vA 278 6.63e+01 1duzA 275 6.72e+01 1agdA b.1.1.2,d.19.1.1 20670,38224 1npsA 88 6.75e+01 1prs b.11.1.1 23622 1gotB 340 6.75e+01 1tbgA b.69.4.1 27648 1wmuB 146 6.76e+01 a.1.1.2 109417 1hgeA 328 6.80e+01 1hgeA b.19.1.2 23816 1tuhA 156 6.81e+01 d.17.4.11 107345 1bsvA 321 6.81e+01 1bsvA c.2.1.2 29809 2bc2B 227 6.81e+01 1a7tA d.157.1.1 42032 2bjrA 368 6.87e+01 1d1gA 168 6.88e+01 1d1gA c.71.1.1 34889 1hkvA 453 6.91e+01 b.49.2.3,c.1.6.1 83559,83560 1i4fA 275 6.91e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 1j9aA 184 6.96e+01 c.55.3.5 84135 1hmvB 440 6.97e+01 1rthA e.8.1.2 43047 1fsyA 358 7.02e+01 1gceA e.3.1.1 60016 2fug1 438 7.06e+01 1fxxA 482 7.13e+01 1fxxA c.55.3.5 33726 1btkB 169 7.22e+01 1btkA b.55.1.1 26960 2bswA 146 7.34e+01 1fvgA 199 7.43e+01 1fvaA d.58.28.1 39408 2gukA 120 7.43e+01 1a97A 148 7.44e+01 1nulA c.61.1.1 34023 1ukvG 453 7.54e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1xdfA 157 7.69e+01 1xn9A 101 7.70e+01 1c25 161 7.73e+01 1c25 c.46.1.1 32698 2ffyA 358 7.73e+01 1oqkA 97 7.79e+01 b.137.1.1 93419 2bcgG 453 7.79e+01 1b8dA 164 7.86e+01 1cpcA a.1.1.3 15665 1ko3A 230 7.86e+01 d.157.1.1 90974 2ai4A 119 7.91e+01 1cz3A 168 7.93e+01 1d1gA c.71.1.1 34891 1wcqA 601 7.94e+01 1dbgA 506 8.01e+01 1dbgA b.80.1.4 28033 1d8iA 311 8.02e+01 1d8iA d.63.1.1 39541 1wmxA 205 8.09e+01 b.18.1.24 109418 1uozA 315 8.11e+01 2blsA 358 8.12e+01 1gceA e.3.1.1 42747 1z7lA 276 8.13e+01 1b37B 472 8.18e+01 1b37B c.3.1.2,d.16.1.5 30390,37954 2carA 196 8.19e+01 1nt4A 391 8.19e+01 c.60.1.2 92102 1q79A 514 8.24e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1dfuP 94 8.24e+01 1dfuP b.53.1.1 26936 2bwqA 129 8.33e+01 1pi4A 358 8.40e+01 e.3.1.1 94700 2ghrA 302 8.40e+01 2d37A 176 8.41e+01 1mwrA 646 8.41e+01 d.17.4.5,d.175.1.1,e.3.1.1 79586,79587,79588 1ygs 234 8.41e+01 1ygs b.26.1.1 23907 1iooA 196 8.41e+01 d.124.1.1 71250 1o6eA 235 8.42e+01 b.57.1.1 81083 1h30A 422 8.69e+01 b.29.1.4,b.29.1.4 76604,76605 1wd6A 123 8.69e+01 2ckiA 262 8.72e+01 1a00B 146 8.77e+01 1abwA a.1.1.2 15469 1zt2B 212 8.82e+01 1ewqA 765 8.88e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1t8hA 277 8.89e+01 d.194.1.2 106664 1l0gA 358 8.89e+01 e.3.1.1 73400 1pvtA 238 8.92e+01 c.74.1.1 95189 1kvlA 358 9.00e+01 e.3.1.1 73062